Contacts of the strand formed by residues 201 - 207 (chain J) in PDB entry 1I43
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 201 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155J HIS* 4.2 11.2 - - + +
157J VAL* 3.5 38.6 - - + +
195J ALA 3.6 23.8 - - - +
196J LEU* 3.7 30.1 + - + +
199J LYS 3.4 1.8 + - - -
200J LYS* 1.3 78.0 - - - +
202J ASN* 1.3 64.0 + - - +
203J LEU 3.7 20.4 - - - +
204J PHE* 4.4 2.2 - - + +
229J LYS 4.7 4.2 + - - +
230J GLY 4.6 2.6 - - - +
231J ALA* 3.6 25.1 + - + +
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Residues in contact with ASN 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149J LEU 5.4 1.0 + - - +
150J VAL* 4.6 8.1 - - + -
151J PRO* 3.7 29.7 - - + +
154J GLY* 3.1 10.9 - - - -
155J HIS 2.9 40.2 + - - +
200J LYS* 3.4 17.3 + - - +
201J VAL* 1.3 73.9 + - - +
203J LEU* 1.3 62.2 + - + +
230J GLY 4.5 2.5 - - - +
231J ALA* 3.8 2.4 - - - -
232J LEU* 3.2 22.2 + - - +
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Residues in contact with LEU 203 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J MET* 3.9 24.0 - - + -
149J LEU* 4.5 16.2 - - + -
150J VAL* 4.0 15.5 - - + -
155J HIS 3.8 1.4 + - - -
156J ILE* 3.2 47.5 - - + +
157J VAL 3.1 21.3 + - - -
201J VAL* 3.6 6.6 - - - +
202J ASN* 1.3 83.3 - - - +
204J PHE* 1.3 64.0 + - - +
205J PHE* 4.0 12.6 - - + -
232J LEU* 3.2 28.3 - - + +
234J CYS* 4.1 18.8 - - + -
254J LEU* 5.0 1.3 - - + -
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Residues in contact with PHE 204 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J VAL* 3.0 43.3 - - + -
158J THR* 4.0 13.5 - - - -
159J THR* 4.3 8.1 - - + -
184J ILE* 4.7 7.2 - - + -
186J PRO 6.1 0.2 - - - -
192J LEU* 3.9 14.6 - - + -
201J VAL* 4.4 2.4 - - + +
203J LEU* 1.3 73.4 - - - +
205J PHE* 1.3 67.5 + - - +
206J THR* 3.5 30.7 - - + -
217J VAL* 4.6 4.5 - - + -
222J VAL* 3.3 44.0 - - + -
226J CYS* 3.7 18.6 - - - -
232J LEU 2.5 14.5 + - - +
233J VAL* 3.5 8.3 - - + -
234J CYS 3.0 25.8 + - - +
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Residues in contact with PHE 205 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J SER* 4.7 8.3 - - - -
145J MET* 4.5 9.0 - - + -
146J LEU* 5.2 5.2 - - + -
156J ILE* 4.6 2.5 - - + -
157J VAL 2.8 9.5 + - - -
158J THR* 3.0 44.7 - - + +
162J CYS* 4.2 13.5 - - - -
166J THR* 3.9 28.0 - - + -
170J ILE* 4.9 4.0 - - + -
203J LEU* 3.9 18.0 + - + -
204J PHE* 1.3 75.0 - - - +
206J THR* 1.3 74.8 + - - +
207J GLU* 4.3 8.1 - - - -
234J CYS* 3.6 23.6 - - + -
236J ASP* 4.5 21.1 - - + -
256J LEU* 3.6 29.2 - - + -
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Residues in contact with THR 206 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J THR* 3.1 30.9 + - - +
162J CYS* 6.3 1.8 - - - -
204J PHE* 3.5 30.1 - - + -
205J PHE* 1.3 86.3 - - - +
207J GLU* 1.3 78.0 + - - +
210J THR* 4.9 0.9 + - - -
217J VAL* 4.2 14.5 - - + +
234J CYS 3.1 3.9 + - - +
235J ILE* 3.1 27.6 - - + -
236J ASP* 2.8 21.9 + - - -
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Residues in contact with GLU 207 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J THR* 5.8 0.2 - - - +
161J ASP 3.5 8.0 - - - +
162J CYS* 4.1 14.7 - - - -
163J TYR* 3.1 35.2 + - - +
205J PHE* 4.3 8.7 - - - -
206J THR* 1.3 87.4 + - - +
208J SER* 1.3 64.5 + - - +
209J PRO 3.3 10.5 - - - +
210J THR* 3.7 22.4 + - - +
211J ASN* 4.0 7.8 + - - +
215J ARG 4.3 1.9 - - - +
217J VAL* 4.7 3.3 - - - +
236J ASP* 3.3 34.1 - - + +
239J PHE* 5.8 0.4 - - + -
500J PLP 3.9 18.7 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il